Detailed information NTG0000261

Experimentally validated

Overview

• Name: lytC
• Type: Auxiliary factor
• Locus tag: KZH43_RS06955
• Genome accession: NZ_CP079923
• Coordinates: 1405971..1407476 (-)
• Length: 501 a.a.
• NCBI ID: WP_075825861.1
• Uniprot ID: Q9Z4J8
• Organism: Streptococcus pneumoniae Rx1
• Function: increase the efficiency of the cell lysis Cell lysis

Function

The two peptidoglycan-hydrolyzing enzymes LytA and LytC, which are present in non-competent target cells, contribute to enhanced lysis during fratricide. Studies have shown that the muralytic activity of CbpD activates LytA and LytC in target cells, thereby accelerating and increasing the efficiency of the lysis reaction

Genomic Context

Location: 1400971..1412476

Locus tag	Gene name	Coordinates (strand)	Size (bp)	Protein ID	Product	Description
KZH43_RS06925 (KZH43_06925)	-	1401900..1402280 (-)	381	WP_001140412.1	RidA family protein	-
KZH43_RS06930 (KZH43_06930)	yihA	1402291..1402878 (-)	588	WP_000422599.1	ribosome biogenesis GTP-binding protein YihA/YsxC	-
KZH43_RS06935 (KZH43_06935)	clpX	1402887..1404119 (-)	1233	WP_220041231.1	ATP-dependent Clp protease ATP-binding subunit ClpX	Regulator
KZH43_RS06940 (KZH43_06940)	-	1404151..1404321 (-)	171	WP_000442275.1	hypothetical protein	-
KZH43_RS06945 (KZH43_06945)	-	1404321..1404827 (-)	507	WP_000162439.1	dihydrofolate reductase	-
KZH43_RS06950 (KZH43_06950)	-	1404957..1405475 (-)	519	WP_000229876.1	DNA starvation/stationary phase protection protein	-
KZH43_RS06955 (KZH43_06955)	lytC	1405971..1407476 (-)	1506	WP_075825861.1	choline binding-anchored murein hydrolase LytC	Auxiliary factor
KZH43_RS06960 (KZH43_06960)	tpiA	1407514..1408272 (-)	759	WP_000087897.1	triose-phosphate isomerase	-
KZH43_RS06965 (KZH43_06965)	-	1408370..1409047 (-)	678	WP_000221615.1	DnaD domain-containing protein	-
KZH43_RS06970 (KZH43_06970)	metA	1409056..1410000 (-)	945	WP_001122712.1	homoserine O-succinyltransferase	-
KZH43_RS06975 (KZH43_06975)	-	1410182..1410694 (-)	513	WP_001049323.1	adenine phosphoribosyltransferase	-
KZH43_RS06980 (KZH43_06980)	-	1410782..1411540 (-)	759	WP_053039685.1	class I SAM-dependent methyltransferase	-
KZH43_RS06985 (KZH43_06985)	-	1411748..1411894 (+)	147	WP_000403100.1	hypothetical protein	-

Regulatory network

Positive effect      

Negative effect

Regulator	Target	Regulation
cbpD	lytC	positive effect
cbpD	lytA	positive effect
comM	cbpD	negative effect
comE	comM	positive effect
comE	comA	positive effect
comA	comC/comC1	positive effect
comE	comB	positive effect
comB	comC/comC1	positive effect
comE	comE	positive effect
comE	comC/comC1	positive effect
comE	comX/comX1	positive effect
comE	comX/comX2	positive effect
comE	comD/comD1	positive effect
comE	comW	positive effect
comD/comD1	comE	positive effect
stkP	comE	positive effect
comC/comC1	comD/comD1	positive effect
ciaR	comC/comC1	negative effect
ciaH	comC/comC1	negative effect
htrA	comC/comC1	negative effect
comX/comX1	late competence genes	positive effect
comW	comX/comX1	positive effect
clpE	comX/comX1	negative effect
clpP	comX/comX1	negative effect
comX/comX2	late competence genes	positive effect
comW	comX/comX2	positive effect
clpE	comX/comX2	negative effect
clpP	comX/comX2	negative effect
clpC	comW	negative effect
clpP	comW	negative effect
mecA	comW	negative effect
ciaR	htrA	positive effect
ciaH	htrA	positive effect
htrA	comEA/celA/cilE	negative effect
htrA	comEC/celB	negative effect
comX/comX1	late competence genes	positive effect
comX/comX2	late competence genes	positive effect

Sequence

Protein

• Length: 501 a.a.
• Molecular weight: 58682.12 Da
• Isoelectric Point: 6.0844

>NTDB_id=261 KZH43_RS06955 WP_075825861.1 1405971..1407476(-) (lytC) [Streptococcus pneumoniae Rx1]
MSVTFFIGEERLKIKIGLASICLLGLATSHVAANETEVAKTSQDTTTASSSSEQNQSSNKTQTSAEVQTNAAAYWDGDYY
VKDDGSKAQSEWIFDNYYKAWFYINSDGRYSQNEWHGNYYLKSGGYMAQNEWIYDSNYKSWFYLKSDGAYAHQEWQLIGN
KWYYFKKWGYMAKSQWQGSYFLNGQGAMIQNEWLYDPAYSAYFYLKSDGTYANQEWQKVGGKWYYFKKWGYMARNEWQGN
YYLTGSGAMATDEVIMDGARYIFAASGELKEKKDLNVGWVHRDGKRYFFNNREEQVGTEHAKKIIDISEHNGRINDWKKV
IDENEVDGVIVRLGYSGKEDKELAHNIKELNRLGIPYGVYLYTYAENETDAENDAKQTIELIKKYNMNLSYPIYYDVENW
EYVNKSKRAPSDTDTWVKIINKYMDTMKQAGYQNVYVYSYRSLLQTRLKHPDILKHVNWVAAYTNALEWENPYYSGEKGW
QYTSSEYMKGIQGRVDVSVWY

Nucleotide

• Length: 1506 bp

>NTDB_id=261 KZH43_RS06955 WP_075825861.1 1405971..1407476(-) (lytC) [Streptococcus pneumoniae Rx1]
ATGTCTGTTACATTTTTTATAGGAGAGGAAAGATTGAAAATAAAAATTGGATTAGCAAGTATCTGTTTACTAGGCTTGGC
AACTAGTCATGTCGCTGCAAATGAAACTGAAGTAGCAAAAACTTCGCAGGATACAACGACAGCTTCAAGTAGTTCAGAGC
AAAATCAGTCTTCTAATAAAACGCAAACGAGCGCAGAAGTACAGACTAATGCTGCTGCCTACTGGGATGGGGATTATTAT
GTAAAGGATGATGGTTCTAAAGCTCAAAGTGAATGGATTTTTGACAACTACTATAAGGCTTGGTTTTATATTAATTCAGA
TGGTCGTTACTCGCAGAATGAATGGCATGGAAATTACTACCTGAAATCAGGTGGATATATGGCCCAAAACGAGTGGATCT
ATGACAGTAATTACAAGAGTTGGTTTTATCTCAAGTCAGATGGGGCTTATGCTCATCAAGAATGGCAATTGATTGGAAAT
AAGTGGTACTACTTCAAGAAGTGGGGTTACATGGCTAAAAGCCAATGGCAAGGAAGTTATTTCTTGAATGGTCAAGGAGC
TATGATACAAAATGAATGGCTCTATGATCCAGCTTATTCTGCTTATTTTTATCTAAAATCCGATGGAACTTATGCTAACC
AAGAGTGGCAAAAAGTGGGCGGCAAATGGTACTATTTCAAGAAGTGGGGCTATATGGCTCGGAATGAGTGGCAAGGCAAC
TACTATTTGACTGGAAGTGGTGCCATGGCGACTGACGAAGTGATTATGGATGGTGCTCGCTATATCTTTGCGGCCTCTGG
TGAGCTCAAAGAAAAGAAAGATTTGAATGTCGGCTGGGTTCACAGAGATGGTAAACGCTATTTCTTTAATAATAGAGAAG
AACAAGTGGGAACCGAACATGCTAAGAAAATCATTGATATTAGTGAGCACAATGGTCGTATCAATGATTGGAAAAAGGTT
ATTGATGAGAACGAGGTGGATGGTGTCATTGTTCGTCTAGGTTATAGCGGTAAAGAAGACAAGGAATTGGCGCATAACAT
TAAGGAGTTAAACCGTCTGGGAATTCCTTATGGTGTCTATCTCTATACCTATGCTGAAAATGAGACCGATGCTGAGAATG
ACGCTAAACAGACCATTGAACTTATAAAGAAATACAATATGAACCTGTCTTACCCTATCTATTATGATGTTGAGAACTGG
GAATATGTAAATAAGAGCAAGAGAGCTCCAAGTGATACAGACACTTGGGTTAAAATCATCAACAAGTACATGGACACGAT
GAAGCAGGCGGGTTATCAAAATGTATATGTCTATAGCTATCGTAGTTTATTACAGACGCGTTTAAAACACCCAGATATTT
TAAAACATGTAAACTGGGTAGCGGCCTATACGAATGCTTTAGAATGGGAAAACCCTTATTATTCAGGAGAAAAAGGTTGG
CAATATACCTCTTCTGAATACATGAAAGGAATCCAAGGGCGCGTAGATGTCAGCGTTTGGTATTAA

Domains

Predicted by InterproScan.

• Glycosyl hydrolases family 25 (Glyco_hydro_25) (305-491)

• Choline-binding repeat (Choline_bind_2) (231-262)

• Putative cell wall binding repeat (Choline_bind_1) (154-171)

• Putative cell wall binding repeat (Choline_bind_1) (91-109)

• Putative cell wall binding repeat (Choline_bind_1) (130-150)

3D structure

• AlphaFold DB: Q9Z4J8

Similar proteins

Only experimentally validated proteins are listed.

Protein	Organism	Identities (%)	Coverage (%)	Ha-value
lytC	Streptococcus pneumoniae D39	100	100	1
lytC	Streptococcus pneumoniae R6	99.8	100	0.998

References

• [1]: Vegard Eldholm et al. (2009) Fratricide in Streptococcus pneumoniae: contributions and role of the cell wall hydrolases CbpD, LytA and LytC. Microbiology (Reading, England) 155(Pt 7):2223-2234. [PMID: 19389766]